Dear Roland, Eventually I installed the installation steps with "./configure --prefix=$HOME/usr "as you said. can you send me the input file for test? I want to run a simulation. how can I do this?
Thanks for your helps 2010/10/2 Roland Schulz <rol...@utk.edu> > Hi, > > either install as root by running: > sudo make install > > or rerun the installation steps with > ./configure --prefix=$HOME/usr > to install it in your home directory. > > Roland > > 2010/10/1 ahmet yıldırım <ahmedo...@gmail.com> > >> Dear justin, >> >> Thanks for your reply. I did that you said. I tried to install Gromacs >> 4.5.1but I failed it. I enter this line " >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 >> make install " in terminal. What can I do? I am sorry. I am a new user. >> >> Thanks in advance >> >> 1. I installed fftw 3.2.2 >> a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2 >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads >> --enable-float >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make >> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install >> >> 2. I tried to install Gromacs 4.5.1 >> a...@ab-desktop:~/Masaüstü/ cd gromacs-4.5.1 >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make >> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make install >> Making install in include >> make[1]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> Making install in . >> make[2]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> make[3]: Entering directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> make[3]: Nothing to be done for `install-exec-am'. >> test -z "/usr/local/gromacs/include/gromacs" || /bin/mkdir -p >> "/usr/local/gromacs/include/gromacs" >> /bin/mkdir: cannot create directory `/usr/local/gromacs': Permission >> denied >> make[3]: *** [install-pkgincludeHEADERS] Error 1 >> make[3]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> make[2]: *** [install-am] Error 2 >> make[2]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> make[1]: *** [install-recursive] Error 1 >> make[1]: Leaving directory `/home/ab/Masaüstü/gromacs-4.5.1/include' >> make: *** [install-recursive] Error 1 >> >> >> >> 2010/10/1 Justin A. Lemkul <jalem...@vt.edu> >> >> >>> >>> ahmet yıldırım wrote: >>> >>>> Hi, >>>> >>>> I've installed GROMACS 4.0.3 and MPI libraries using Ubuntu 9.04 >>>> Synaptic Package Manager. What else should I do? >>>> I want to run a simulation in parallel on a single PC. Which commands >>>> should I enter the terminal? >>>> >>>> >>> If I were you, I would uninstall this version (which is outdated by >>> nearly 2 years!) and get version 4.5.1. Installing from source is quite >>> easy. Not only will you benefit from hundreds of bug fixes and >>> enhancements, but running in parallel on a multi-core machine is no longer >>> MPI-dependent, making it somewhat easier. >>> >>> For usage and instructions, see the manual and any of the numerous >>> tutorials linked here: >>> >>> http://www.gromacs.org/Documentation/Tutorials#General >>> >>> -Justin >>> >>> >>> Thanks a lot for any instruction. >>>> >>>> >>>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the www >>> interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Ahmet YILDIRIM >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov > 865-241-1537, ORNL PO BOX 2008 MS6309 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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